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Yorodumi- PDB-1lr8: Crystal structure of Fs1, the heparin-binding domain of follistat... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1lr8 | ||||||
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Title | Crystal structure of Fs1, the heparin-binding domain of follistatin, complexed with the heparin analogue D-myo-inositol hexasulphate (Ins6S) | ||||||
Components | Follistatin | ||||||
Keywords | HORMONE/GROWTH FACTOR / cystine-rich / D-myo-inositol hexasulphate / HORMONE-GROWTH FACTOR COMPLEX | ||||||
Function / homology | Function and homology information Antagonism of Activin by Follistatin / activin receptor antagonist activity / negative regulation of follicle-stimulating hormone secretion / ameloblast differentiation / positive regulation of hair follicle development / regulation of BMP signaling pathway / gamete generation / pattern specification process / activin binding / negative regulation of activin receptor signaling pathway ...Antagonism of Activin by Follistatin / activin receptor antagonist activity / negative regulation of follicle-stimulating hormone secretion / ameloblast differentiation / positive regulation of hair follicle development / regulation of BMP signaling pathway / gamete generation / pattern specification process / activin binding / negative regulation of activin receptor signaling pathway / heparan sulfate proteoglycan binding / negative regulation of epithelial cell differentiation / hair follicle morphogenesis / female gonad development / BMP signaling pathway / odontogenesis of dentin-containing tooth / keratinocyte proliferation / hematopoietic progenitor cell differentiation / skeletal system development / response to organic cyclic compound / cellular response to growth factor stimulus / cell differentiation / negative regulation of transcription by RNA polymerase II / extracellular space / extracellular region / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Innis, C.A. / Hyvonen, M. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2003 Title: Crystal Structures of the Heparan Sulfate-binding Domain of Follistatin: Insights into ligand binding. Authors: Innis, C.A. / Hyvonen, M. | ||||||
History |
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Remark 600 | heterogen authors informed that the inositol ring is missing from the ligand d-myo-inositol ... heterogen authors informed that the inositol ring is missing from the ligand d-myo-inositol hexasulphate due to lack of connecting electron density. Authors state this may be due to a superimposition of inositol molecules bound in alternative ways. Although specific numbering of the ligand is present, the observed sulphate groups may correspond to one or several instances of a bound sulphate, and thus numbering of the groups is somewhat arbitrary. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1lr8.cif.gz | 28.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1lr8.ent.gz | 17.9 KB | Display | PDB format |
PDBx/mmJSON format | 1lr8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1lr8_validation.pdf.gz | 810.1 KB | Display | wwPDB validaton report |
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Full document | 1lr8_full_validation.pdf.gz | 810.8 KB | Display | |
Data in XML | 1lr8_validation.xml.gz | 5.8 KB | Display | |
Data in CIF | 1lr8_validation.cif.gz | 7.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lr/1lr8 ftp://data.pdbj.org/pub/pdb/validation_reports/lr/1lr8 | HTTPS FTP |
-Related structure data
Related structure data | 1lr7SC 1lr9C S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 8342.812 Da / Num. of mol.: 1 / Fragment: heparin-binding domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Plasmid: pBAT4 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P21674 |
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#2: Chemical | ChemComp-IHS / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.96 Å3/Da / Density % sol: 35.85 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 15-25% PEG8000, 0.2-0.6 M Magnesium acetate, 0.1 M Sodium cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 18 ℃ / pH: 8.5 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9202 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 4, 2001 / Details: mirrors |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9202 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→38.9 Å / Num. obs: 4026 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 19.44 Å2 / Rmerge(I) obs: 0.081 |
Reflection shell | Resolution: 2.1→2.18 Å / Rmerge(I) obs: 0.206 / % possible all: 99.7 |
Reflection | *PLUS % possible obs: 98.6 % / Rmerge(I) obs: 0.08 |
Reflection shell | *PLUS % possible obs: 99.7 % / Rmerge(I) obs: 0.26 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1LR7 Resolution: 2.1→38.92 Å / Cor.coef. Fo:Fc: 0.917 / Cor.coef. Fo:Fc free: 0.883 / SU B: 6.951 / SU ML: 0.189 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.299 / ESU R Free: 0.212 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.635 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→38.92 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.154 Å / Total num. of bins used: 20
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Refinement | *PLUS Lowest resolution: 38.9 Å / Num. reflection obs: 3801 / Rfactor Rfree: 0.251 / Rfactor Rwork: 0.221 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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